I talked to someone last year who was engaged in a DIY fecal transplant. There are good reasons why NOT to do this yourself. For the recent study on ulcerative colitis patients, which had great success, the donors were screened* as follows:
hepatitis A IgM, hepatitis B surface Ag, hepatitis B surface Ab, hepatitis B core Ab, hepatitis C Ab, EBV VCA IgM, CMV IgM, syphilis IgG, HIV I and II ELISA
Stool culture for Salmonella, Shigella, E. coli, Campylobacter, Yersinia, Vibrio, and Listeria, C. difficile toxin PCR, ova and parasite screening, fungal smear.
In other words, any donors should be properly screened--there is no reason to risk infection. Discuss this option with a doctor.
This is a relatively low-cost, high impact type of treatment which is happening all over he country. (Although unpublished, yesterday I heard of high success rate with pediatric Crohn's patients in Seattle undergoing fecal transplant.)
*Kunde, S., Pham, A., Bonczyk, S., Teri, C., Duba, M., Conrad, H., Cloney, D., et al. (2013). Safety, Tolerability, and Clinical Response after Fecal Transplantation in Children and Young Adults with Ulcerative Colitis. Journal of pediatric gastroenterology and nutrition, (616). doi:10.1097/MPG.0b013e318292fa0d